[maker-devel] Maker MPI across nodes

[James Cross (ITCS - Staff)]

Hi Maker Developers,

We are trying to run Maker with OpenMPI on our HPC cluster across two nodes (each node containing 28 Core's so 56 Core's in total). While Maker seems to be running correctly its going slower when split across two nodes (56 Core's) as opposed to being run on a single node (28 Core's). We are trying to increase the speed that Maker will complete its run in. Do you know of any reason for why Maker might slow down when split across two nodes?

Our cluster OS is: CentOS 6.7 and the HPC scheduler used is: LSF. We are running Open mpi on a Mellanox Infiniband network.

The genome data we wish to annotate is comprised of 1948 scaffolds with an average length of 324890bp (longest scaffold 6948830bp).

The command in batch mode we are using is: mpiexec -mca btl ^openib -n 56 maker

Any help or advise you could give would be greatly appreciated.

Best Wishes
Jimmy
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Mr  James Cross
HPC Systems Developer
University of East Anglia
Norwich Research Park
ITCS
Norwich, Norfolk
NR4 7TJ

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